Arabidopsis-rice: will colinearity allow gene prediction across the eudicot-monocot divide?

With the genomic sequencing of Arabidopsis nearing completion and rice sequencing very much in its infancy, a key question is whether we can exploit the Arabidopsis sequence to identify candidate genes for traits in cereal crops using a map-based approach. This requires the existence of colinearity between the Arabidopsis and cereal genomes, represented by rice, which is readily detectable using currently available resources, that is, Arabidopsis genomic sequence, rice ESTs, and genetic and physical maps. A detailed study of the colinearity remaining between two small regions of Arabidopsis chromosome 1 and rice suggests that at least in these regions of the Arabidopsis genome, conservation of gene orders with rice has been eroded to the point that it is no longer identifiable using comparative mapping. Although our analysis does not preclude that tracts of colinear gene orders may be identified using sequence comparisons or may exist in other regions of the rice and Arabidopsis genomes, it is unlikely that the extent of colinearity will be sufficient to allow map-based cross-species gene prediction and isolation. Our research also highlights the difficulties encountered in identifying orthologs using BLAST searches in incomplete sequence databases. This complicates the interpretation of comparative data among highly divergent species and limits the exploitation of Arabidopsis sequence in monocot studies.